This paper is concerned with inter-subject registration of anatomical and functional brain data, and extends our previouswork [7] on evaluation of intersubject registration methods. The paper evaluates the SPM spatial normalization method [1], which is widely used by the neuroscience community. This paper also extends the previous evaluation framework to functional MEG data. The impact of three different registration methods on the registration of somatosensory MEG data is studied.We showthat the inter-subject functional variability can be reduced with inter-subject non-rigid registration methods, which is in accordance with the hypothesis that part of the inter-subject functional variability is encoded in the inter-subject anatomical variability.